WASHINGTON — The flaws in the American election system are deep and widespread, extending beyond isolated voting issues in a few locations and flaring up in states rich and poor, according to a major new study from the Pew Charitable Trusts.

The group ranked all 50 states based on more than 15 criteria, including wait times, lost votes and problems with absentee and provisional ballots, and the order often confounds the conventional wisdom.

In 2010, for instance, Mississippi ranked last over all. But it was preceded by two surprises: New York and California.

“Poor Southern states perform well, and they perform badly,” said Heather K. Gerken, a law professor at Yale and a Pew adviser. “Rich New England states perform well and badly — mostly badly.”

The project includes an interactive tool that allows rankings by individual criteria or clusters of them.

Some states, for instance, lost very few votes because of shortcomings in voting technology and voter confusion, with the best 10 reporting failure rates of 0.5 percent or less in 2008. In West Virginia, by contrast, the rate was 3.2 percent.

Natalie Tennant, West Virginia’s secretary of state, said she was not happy with that result and would look closely at Pew’s data and methodology. But she added that “2012 went really well, even with Sandy,” referring to the hurricane that disrupted early voting. “We were humming,” she said.

“You’re only as good as your next election,” she added.

The Pew study focused on the 2008 and 2010 elections, the most recent ones for which comprehensive data were available.

The study also found wide variation in how easy registering to vote can be. North Dakota does not even require it, and Alabama and Kansas reported rejecting less than 0.05 percent of registration applications in 2008. But Pennsylvania and Indiana each rejected more than half of the registration applications they received in 2010.

On Election Day, the voting experience can also vary. The 10 states with the shortest waiting times at the polls in 2008 averaged six minutes, the study found. In South Carolina, the wait was more than an hour.

The shift to voting by mail, which now accounts for some 20 percent of all ballots cast, tends to eliminate lines. But it has also produced new problems, especially in places where mail voting has soared because the state does not require an excuse or a new ballot request for each election. Arizona and California, where voting by mail is commonplace, had among the highest rates of problems with voter registration and absentee ballots.

In 2010, California rejected absentee ballots 0.7 percent of the time, a higher rate than any other state.

Dean C. Logan, the registrar for Los Angeles County, said the rate was partly a byproduct of the popularity of voting by mail in California and partly a function of how the state defines rejected ballots. Its definition includes ballots that voters requested but that the Postal Service returned to election officials as undeliverable.

“Voter behavior is changing and evolving,” Mr. Logan said. Young people do not sign their names as consistently as older ones, he said, and mail delivery is becoming less reliable.

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He also cautioned that statewide results can mask the fact that “the elections process is extremely decentralized.”

Colorado, where some 70 percent of voters cast their ballots by mail in 2012, rejected absentee ballots 0.4 percent of the time in 2010.

Pam Anderson, the clerk of Jefferson County, Colo., defended that rejection rate. “It’s not 10 percent, and it’s not zero,” she said. “We do a very rigorous signature verification process.”

Charles Stewart III, a political scientist at the Massachusetts Institute of Technology and a Pew adviser, said that high provisional ballot rates were an important signal of potential trouble.

“Nationwide, a bit over 1 percent of voters are given a provisional ballot,” he said. “In Arizona in 2008, the rate was 6.5 percent. In the battleground state of Ohio, it was 3.6 percent. While these numbers may seem small, in a recount or election dispute, they would be huge.”

In both 2008 and 2010, Arizona had the highest rate of rejected provisional ballots, though the rate dropped to 0.8 percent in 2010 from 1.9 percent in 2008.

Tammy Patrick, an elections official in Maricopa County, Ariz., said that last year “65 percent of people voted by mail, which is grand.”

Ms. Patrick said that voting by mail gave voters the benefit of convenience, and also the ability to reflect on their choices. “We have a fairly long ballot,” she said, “and this allows the voter a full month to vote that ballot.”

But the trend also led to problems, Ms. Patrick said, partly as a result of grass-roots misinformation about whether and how such votes would be counted.

Many people voted by mail and nonetheless turned up at polling places just in case, where they would often cast provisional ballots. “We had a 20 percent increase in our provisional ballots over all,” Ms. Patrick said, and many of those ballots were rejected.

She said that the Pew data reflected “a piece of what we do,” but that the local political culture also played a role. “Arizonans don’t feel their elected officials represent them,” she said. “They don’t participate in their neighborhoods and civic activities. There’s a detachment in the sprawl.”

Professor Gerken said that other cultural factors may affect voting rates. “States in the Deep South with high obesity problems seem to be having a problem getting people to the polling place,” she said.

Absentee ballots from members of the military and Americans living overseas were also rejected at varying rates, the study found. In 2010, New York rejected a quarter of the 22,000 such ballots it received. Pennsylvania rejected just 2 percent of the 8,000 ballots it received.

Professor Stewart said the study should focus attention on the infrastructure of democracy.

“Among all important areas of public policy, election administration is probably the most episodic and prone to the problem of short attention spans,” he said. “What would the world be like if we only gave intense attention to education, corrections, transportation and public health problems for a one-week period every four years?”

A version of this article appears in print on February 6, 2013, on Page A17 of the New York edition with the headline: Lost Votes, Problem Ballots, Long Waits? Flaws Are Widespread, Study Finds. Order Reprints|Today's Paper|Subscribe